Code:
ÂÂÂÂ ------- Hard drive 1
ÂÂÂÂ |
PC----|
ÂÂÂÂ |
ÂÂÂÂ ------- Hard drive 2
(hopefully that appears OK)
Unless you use raid0 (which is not suggested for this scenario) windows will be on one drive (for the sake of this example I am using Hard drive 1)
Everything windows does will cause hard drive 1 to be accessed.
The electromechanical nature of hard drives means that trying to access several things at once from one drive means a fair bit of slowdown as the heads reposition.
As windows is always running hard drive 1 will always be being accessed, you can not easily change it so some necessary windows files files are on one drive and some more on the other in an attempt to dodge this or spread the load.
You can change the location of programs, documents, music and whatever else (in this case you would want them on hard drive 2) but given windows should not take more than about 10 gigabytes (probably more like 3) I am guessing while you can/will mainly use hard drive 2 for day to day stuff, installation folders and storage the time will come (and believe me it will) when you do not want to "lose"/ignore the 900 odd gigabytes not used on hard drive 1.
Granted windows will occasionally not need as much hard drive time but the small amount it does need will drag down everything else from time to time (for single hard drive computers this is a frequent source of slowdown in games or big videos: I am sure we have been there when an AV scan kicks in during the middle of something).
The same idea does apply to raid0 (perhaps even more so as it is effectively one drive) but it is/should be that much faster that any penalties for this sort of thing are reduced to the point where it does not matter without you having to think about what goes on what drive (not a difficult feat or one you will ever really have to engage in if you are not running raid0).
Partitions will help with fragmentation (a big part of the problem) but as the drive is still in the same physical package regardless of how many partitions you have the time penalty is still there.